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nolanlab / citrus

Citrus Development Code
GNU General Public License v3.0
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gcc48 issue #91

Closed chethanjjj closed 8 years ago

chethanjjj commented 8 years ago

installed Citrus, however it crashed my RStudio anytime I ran it, so I followed your directions to install Citrus using MacPorts with g++4.8, however after running the following code:

sudo port install gcc48

I got the following error:

Error: org.macports.build for port gcc48 returned: command execution failed Please see the log file for port gcc48 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc48/gcc48/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port gcc48 failed

After reading forums, the error seems to be involved with the updated Mac OS Software: El Capitan. Do you have any thoughts about a way around this?

I've also included my terminal commands in a text file attachment, so you can see exactly what happened

Log at 2016-01-18 23.17.34.txt

rbruggner commented 8 years ago

I was able to replicate this issue, but really don't have a good suggestion at the moment for working around the problem. Have you tried installing / using another version of GCC - say 4.9?

I have no idea if that would work, but that's the only thing that comes to mind immediately.

SamGG commented 8 years ago

Did you look at https://trac.macports.org/ticket/48471? They report also their trials in getting higher versions of gcc, but BLAS seems to require 4.8. It seems (3h ago) to be fixed in Xcode 7.3, but I don't have any Mac...

chethanjjj commented 8 years ago

I tried 4.9 and citrus installed without a problem and didn't crash when I used it, so it seems to be working fine.

chethanjjj commented 8 years ago

Thank you for taking the time to review this problem, Dr. Bruggner.

chethanjjj commented 8 years ago

Hi Dr. Bruggner,

After following your suggestion about gcc49, I found that flowStats and openCyto (bioconductor packages) would crash whenever I tried to load them.

I traced this issue to the following line of code: install.packages(c("Rcpp","RcppEigen","Rclusterpp"),type="source")

FlowStats and openCyto will only work properly if I install the binary packages or install the source packages via the clang++ compiler.

so now my temporary solution to use flowStats/openCyto and CITRUS is to recompile these packages with gcc49 for CITRUS use and clang++/use binary packages for flowStats/openCyto use.

Do you have any possible solution, so that I won't have to do this?

rbruggner commented 8 years ago

As @SamGG mentioned (thanks!), this issue might be fixed in Xcode 7.3 (as per this comment https://trac.macports.org/ticket/48471#comment:92). If you download and install Xcode 7.3 (https://developer.apple.com/xcode/download/), it might enable you to install GCC 4.8 which I believe would resolve the crashes.

However, I have not verified that installing XCode 7.3 does indeed fix the problem with installing GCC 4.8.

chethanjjj commented 8 years ago

i see. hmmm ok. well when I get a chance I will test this out and get back to you guys!

rbruggner commented 8 years ago

Apple just officially released XCode 7.3 today. I installed it and confirmed that you can now properly build GCC 4.8 from mac ports.

chethanjjj commented 8 years ago

Oh sweet. Thanks Rob!

On Mar 21, 2016, at 2:00 PM, Robert Bruggner notifications@github.com wrote:

Apple just officially released XCode 7.3 today. I installed it and confirmed that you can now properly build GCC 4.8 from mac ports.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub